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The water level is low at Anderson Reservoir in Morgan Hill, Calif., Oct. 1,… ( Patrick Tehan )

LOS BANOS — Robert Haskins walked across a vast expanse of cracked mud, littered with old beer bottles and millions of tiny clam shells, that in most Augusts would be 50 feet underwater.

But the San Luis Reservoir, the vast inland sea along Highway 152 that is a key part of Silicon Valley’s water supply, is only 10 percent full, its lowest level in 27 years.

“Normally that’s an island,” the Santa Clara Valley Water District maintenance supervisor said, pointing to a towering hill.

The nation’s largest off-stream reservoir is high and dry this summer, and it’s not really because of the drought. Northern California received its most rain in five years this winter.

The water level is low at Anderson Reservoir in Morgan Hill, Calif., Oct. 1, 2015 due to the ongoing drought. (Patrick Tehan/Bay Area News Group)

The water level is low at Anderson Reservoir in Morgan Hill, Calif., Oct. 1, 2015 due to the ongoing drought. (Patrick Tehan/Bay Area News Group) ( Patrick Tehan )

Instead, a “perfect storm” of controversial human causes — from an attempt to save endangered salmon hundreds of miles away, to age-old water rights that give rice growers near Sacramento the water first — has left the state’s fifth-largest reservoir so low that the last time some now-dry areas were exposed to the air, George Bush Sr. was president, Joe Montana was quarterback of the 49ers and the Loma Prieta earthquake hadn’t happened yet.

“It is extremely frustrating,” said Melih Ozbilgin, a senior water resources specialist with the district.

 Some relief may occur in about a month. But for now, not only has the situation enraged farmers, it has sparked algae problems and other headaches for nearly 2 million residents of Santa Clara County who drink the water.
 What’s difficult for many people to grasp is how the massive reservoir could be so low after this winter’s rains.

One of the most contentious reasons is the effort to save an endangered fish.

Even though the state’s largest reservoir, Shasta Lake, near Redding, is 75 percent full, federal officials reduced the rate this summer at which they would normally release water from it. In a typical year, water would pour out of Shasta, down the Sacramento River to the Delta, and some would be drawn from pumps near Tracy to be put into San Luis, about 75 miles south of the Delta.

But this summer, in an effort to protect endangered winter-run Chinook salmon, the National Marine Fisheries Service required the U.S. Bureau of Reclamation to cut flows from Shasta from roughly 13,000 cubic feet per second to 10,500.

The idea was to preserve plenty of cold water, which sits deep in the Shasta reservoir, so that it could be released steadily throughout the summer at about 52 degrees, helping the endangered fish eggs and young fish survive in the Sacramento River.

Environmentalists say the decision was a good one. The iconic fish suffered terrible losses last year and the year before, in part because of the drought, but also because of water management.

“The past two years, they ran out of cold water in Shasta, and the water got so hot it fried virtually all of the salmon,” said Doug Obegi, an attorney with the San Francisco-based Natural Resources Defense Council. “Because the salmon that are returning this year are perhaps the last winter-run that exist in nature, they are being more conservative. This is the last of the last.”

But farmers say the bureau and the fisheries service are being overly cautious. They produced charts and graphs to bolster their contentions that cold temperatures can be maintained with less water in Shasta.

“The unending practice of taking water from human use and giving it to fish in hopes of helping the fish is a failed enterprise,” said Jason Peltier, executive director of the San Luis & Delta-Mendota Water Authority, which represents San Joaquin Valley farmers. “The fish are not responding at all. At the same time human, social and economic destruction continues to accelerate. Shameful.”

Shane Hunt, a spokesman for the Bureau of Reclamation, said the agency has to follow the Endangered Species Act.

“People are constantly wanting us to do something different than we are doing, whether it is the environmental groups, the recreation community or the water community,” he said. “We are still dealing with the lingering effects of the drought and how that has impacted our water users, the environment and our reservoir system. There are very difficult decisions being made.”

A second problem for San Luis is that large amounts of the water that does come out of Shasta are taken by people with senior water rights before the water ever gets to the Delta, like farmers growing rice, walnuts and other crops in the Glenn-Colusa Irrigation District and other areas in the Sacramento Valley.

Third, the rain and snow wasn’t evenly distributed this winter. The southern Sierra received less than the northern Sierra. So runoff into the San Joaquin River, which flows into the Delta, was limited. And after five years of drought, farmers and communities along the river and on Sierra rivers that feed into the San Joaquin, also with senior water rights, have been diverting water for their own use.

That’s left very little freshwater flowing now from the San Joaquin River into the Delta. On top of that, two king tides in July pushed saltwater from the ocean farther east into the Delta. State water quality standards designed to keep drinking and farm irrigation water from getting too salty required that lots of freshwater stay in the Delta, rather than it being pumped into San Luis, to dilute the salty water.

Some good news is on the horizon. Already, farmers are beginning to use less water because the growing season is winding down, so there is more freshwater in the Delta. That should allow more to be pumped into San Luis Reservoir in the coming month, said Hunt.

Santa Clara County won’t run out of water. It has more than a year’s supply in underground aquifers and more in local reservoirs. But the issue has caused problems. Elevated levels of algae, while safe to drink, have caused some taste and odor complaints and clogged filters at treatment plants. The limited amount of San Luis water also has reduced the rate at which Santa Clara County’s underground aquifers can be recharged.

For Haskins, who visited the lake bottom this week, one thing was clear.

“No one,” he said, “likes to see our water supplies dwindle like this.”